From 56078b6b44f3a3e724f3ec2e3173075ab9043310 Mon Sep 17 00:00:00 2001
From: Marti Bolivar <mbolivar@mit.edu>
Date: Mon, 11 Oct 2010 20:02:04 -0400
Subject: more docs

---
 Doxyfile                     | 1634 ++++++++++++++++++++++++++++++++++++++++++
 README                       |   41 +-
 source/adc.rst               |   70 +-
 source/bootloader.rst        |    3 +
 source/compatibility.rst     |  129 ++++
 source/conf.py               |   22 +-
 source/epilog.rst            |   51 ++
 source/errata.rst            |   11 +
 source/gpio.rst              |   89 ++-
 source/i2c.rst               |    2 -
 source/language.rst          |   53 +-
 source/libmaple-api.rst      |    1 +
 source/libmaple.rst          |    2 +
 source/libraries.rst         |    4 +-
 source/maple-ide-install.rst |    3 +-
 source/maple-quickstart.rst  |    9 +-
 source/prolog.rst            |    7 +
 source/troubleshooting.rst   |  275 ++++---
 18 files changed, 2183 insertions(+), 223 deletions(-)
 create mode 100644 Doxyfile
 create mode 100644 source/prolog.rst

diff --git a/Doxyfile b/Doxyfile
new file mode 100644
index 0000000..73f18f9
--- /dev/null
+++ b/Doxyfile
@@ -0,0 +1,1634 @@
+# Doxyfile 1.7.1
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+#       TAG = value [value, ...]
+# For lists items can also be appended using:
+#       TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file 
+# that follow. The default is UTF-8 which is also the encoding used for all 
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the 
+# iconv built into libc) for the transcoding. See 
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
+# by quotes) that should identify the project.
+
+PROJECT_NAME           = libmaple
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
+# This could be handy for archiving the generated documentation or 
+# if some version control system is used.
+
+PROJECT_NUMBER         = custom-build
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
+# base path where the generated documentation will be put. 
+# If a relative path is entered, it will be relative to the location 
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = ./docs/doxygen
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
+# 4096 sub-directories (in 2 levels) under the output directory of each output 
+# format and will distribute the generated files over these directories. 
+# Enabling this option can be useful when feeding doxygen a huge amount of 
+# source files, where putting all generated files in the same directory would 
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS         = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
+# documentation generated by doxygen is written. Doxygen will use this 
+# information to generate all constant output in the proper language. 
+# The default language is English, other supported languages are: 
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, 
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English 
+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, 
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, 
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+
+OUTPUT_LANGUAGE        = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
+# include brief member descriptions after the members that are listed in 
+# the file and class documentation (similar to JavaDoc). 
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
+# the brief description of a member or function before the detailed description. 
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator 
+# that is used to form the text in various listings. Each string 
+# in this list, if found as the leading text of the brief description, will be 
+# stripped from the text and the result after processing the whole list, is 
+# used as the annotated text. Otherwise, the brief description is used as-is. 
+# If left blank, the following values are used ("$name" is automatically 
+# replaced with the name of the entity): "The $name class" "The $name widget" 
+# "The $name file" "is" "provides" "specifies" "contains" 
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF       = "The $name class" \
+                         "The $name widget" \
+                         "The $name file" \
+                         is \
+                         provides \
+                         specifies \
+                         contains \
+                         represents \
+                         a \
+                         an \
+                         the
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
+# Doxygen will generate a detailed section even if there is only a brief 
+# description.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all 
+# inherited members of a class in the documentation of that class as if those 
+# members were ordinary class members. Constructors, destructors and assignment 
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
+# path before files name in the file list and in the header files. If set 
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES        = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
+# can be used to strip a user-defined part of the path. Stripping is 
+# only done if one of the specified strings matches the left-hand part of 
+# the path. The tag can be used to show relative paths in the file list. 
+# If left blank the directory from which doxygen is run is used as the 
+# path to strip.
+
+STRIP_FROM_PATH        = 
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of 
+# the path mentioned in the documentation of a class, which tells 
+# the reader which header file to include in order to use a class. 
+# If left blank only the name of the header file containing the class 
+# definition is used. Otherwise one should specify the include paths that 
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH    = 
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
+# (but less readable) file names. This can be useful is your file systems 
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
+# will interpret the first line (until the first dot) of a JavaDoc-style 
+# comment as the brief description. If set to NO, the JavaDoc 
+# comments will behave just like regular Qt-style comments 
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF      = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will 
+# interpret the first line (until the first dot) of a Qt-style 
+# comment as the brief description. If set to NO, the comments 
+# will behave just like regular Qt-style comments (thus requiring 
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
+# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
+# comments) as a brief description. This used to be the default behaviour. 
+# The new default is to treat a multi-line C++ comment block as a detailed 
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
+# member inherits the documentation from any documented member that it 
+# re-implements.
+
+INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce 
+# a new page for each member. If set to NO, the documentation of a member will 
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE               = 4
+
+# This tag can be used to specify a number of aliases that acts 
+# as commands in the documentation. An alias has the form "name=value". 
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
+# put the command \sideeffect (or @sideeffect) in the documentation, which 
+# will result in a user-defined paragraph with heading "Side Effects:". 
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES                = "sideeffect=\par Side Effects:\n"
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C 
+# sources only. Doxygen will then generate output that is more tailored for C. 
+# For instance, some of the names that are used will be different. The list 
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C  = YES
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
+# sources only. Doxygen will then generate output that is more tailored for 
+# Java. For instance, namespaces will be presented as packages, qualified 
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran 
+# sources only. Doxygen will then generate output that is more tailored for 
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN   = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL 
+# sources. Doxygen will then generate output that is tailored for 
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it 
+# parses. With this tag you can assign which parser to use for a given extension. 
+# Doxygen has a built-in mapping, but you can override or extend it using this 
+# tag. The format is ext=language, where ext is a file extension, and language 
+# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C, 
+# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make 
+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C 
+# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions 
+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+
+EXTENSION_MAPPING      = 
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want 
+# to include (a tag file for) the STL sources as input, then you should 
+# set this tag to YES in order to let doxygen match functions declarations and 
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
+# func(std::string) {}). This also make the inheritance and collaboration 
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to 
+# enable parsing support.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. 
+# Doxygen will parse them like normal C++ but will assume all classes use public 
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT            = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate getter 
+# and setter methods for a property. Setting this option to YES (the default) 
+# will make doxygen to replace the get and set methods by a property in the 
+# documentation. This will only work if the methods are indeed getting or 
+# setting a simple type. If this is not the case, or you want to show the 
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT   = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
+# tag is set to YES, then doxygen will reuse the documentation of the first 
+# member in the group (if any) for the other members of the group. By default 
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
+# the same type (for instance a group of public functions) to be put as a 
+# subgroup of that type (e.g. under the Public Functions section). Set it to 
+# NO to prevent subgrouping. Alternatively, this can be done per class using 
+# the \nosubgrouping command.
+
+SUBGROUPING            = YES
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
+# is documented as struct, union, or enum with the name of the typedef. So 
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct 
+# with name TypeT. When disabled the typedef will appear as a member of a file, 
+# namespace, or class. And the struct will be named TypeS. This can typically 
+# be useful for C code in case the coding convention dictates that all compound 
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT   = YES
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to 
+# determine which symbols to keep in memory and which to flush to disk. 
+# When the cache is full, less often used symbols will be written to disk. 
+# For small to medium size projects (<1000 input files) the default value is 
+# probably good enough. For larger projects a too small cache size can cause 
+# doxygen to be busy swapping symbols to and from disk most of the time 
+# causing a significant performance penality. 
+# If the system has enough physical memory increasing the cache will improve the 
+# performance by keeping more symbols in memory. Note that the value works on 
+# a logarithmic scale so increasing the size by one will rougly double the 
+# memory usage. The cache size is given by this formula: 
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, 
+# corresponding to a cache size of 2^16 = 65536 symbols
+
+SYMBOL_CACHE_SIZE      = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
+# documentation are documented, even if no documentation was available. 
+# Private class members and static file members will be hidden unless 
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
+# will be included in the documentation.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file 
+# will be included in the documentation.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
+# defined locally in source files will be included in the documentation. 
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. When set to YES local 
+# methods, which are defined in the implementation section but not in 
+# the interface are included in the documentation. 
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS  = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be 
+# extracted and appear in the documentation as a namespace called 
+# 'anonymous_namespace{file}', where file will be replaced with the base 
+# name of the file that contains the anonymous namespace. By default 
+# anonymous namespace are hidden.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
+# undocumented members of documented classes, files or namespaces. 
+# If set to NO (the default) these members will be included in the 
+# various overviews, but no documentation section is generated. 
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
+# undocumented classes that are normally visible in the class hierarchy. 
+# If set to NO (the default) these classes will be included in the various 
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
+# friend (class|struct|union) declarations. 
+# If set to NO (the default) these declarations will be included in the 
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
+# documentation blocks found inside the body of a function. 
+# If set to NO (the default) these blocks will be appended to the 
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation 
+# that is typed after a \internal command is included. If the tag is set 
+# to NO (the default) then the documentation will be excluded. 
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
+# file names in lower-case letters. If set to YES upper-case letters are also 
+# allowed. This is useful if you have classes or files whose names only differ 
+# in case and if your file system supports case sensitive file names. Windows 
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES       = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
+# will show members with their full class and namespace scopes in the 
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
+# will put a list of the files that are included by a file in the documentation 
+# of that file.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen 
+# will list include files with double quotes in the documentation 
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
+# is inserted in the documentation for inline members.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
+# will sort the (detailed) documentation of file and class members 
+# alphabetically by member name. If set to NO the members will appear in 
+# declaration order.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the 
+# brief documentation of file, namespace and class members alphabetically 
+# by member name. If set to NO (the default) the members will appear in 
+# declaration order.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen 
+# will sort the (brief and detailed) documentation of class members so that 
+# constructors and destructors are listed first. If set to NO (the default) 
+# the constructors will appear in the respective orders defined by 
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. 
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO 
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = YES
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the 
+# hierarchy of group names into alphabetical order. If set to NO (the default) 
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
+# sorted by fully-qualified names, including namespaces. If set to 
+# NO (the default), the class list will be sorted only by class name, 
+# not including the namespace part. 
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. 
+# Note: This option applies only to the class list, not to the 
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or 
+# disable (NO) the todo list. This list is created by putting \todo 
+# commands in the documentation.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or 
+# disable (NO) the test list. This list is created by putting \test 
+# commands in the documentation.
+
+GENERATE_TESTLIST      = NO
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or 
+# disable (NO) the bug list. This list is created by putting \bug 
+# commands in the documentation.
+
+GENERATE_BUGLIST       = NO
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
+# disable (NO) the deprecated list. This list is created by putting 
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional 
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS       = 
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
+# the initial value of a variable or define consists of for it to appear in 
+# the documentation. If the initializer consists of more lines than specified 
+# here it will be hidden. Use a value of 0 to hide initializers completely. 
+# The appearance of the initializer of individual variables and defines in the 
+# documentation can be controlled using \showinitializer or \hideinitializer 
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
+# at the bottom of the documentation of classes and structs. If set to YES the 
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES        = YES
+
+# If the sources in your project are distributed over multiple directories 
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES       = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. 
+# This will remove the Files entry from the Quick Index and from the 
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the 
+# Namespaces page.  This will remove the Namespaces entry from the Quick Index 
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that 
+# doxygen should invoke to get the current version for each file (typically from 
+# the version control system). Doxygen will invoke the program by executing (via 
+# popen()) the command <command> <input-file>, where <command> is the value of 
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
+# provided by doxygen. Whatever the program writes to standard output 
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER    = 
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed 
+# by doxygen. The layout file controls the global structure of the generated 
+# output files in an output format independent way. The create the layout file 
+# that represents doxygen's defaults, run doxygen with the -l option. 
+# You can optionally specify a file name after the option, if omitted 
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE            = 
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated 
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are 
+# generated by doxygen. Possible values are YES and NO. If left blank 
+# NO is used.
+
+WARNINGS               = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
+# potential errors in the documentation, such as not documenting some 
+# parameters in a documented function, or documenting parameters that 
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be abled to get warnings for 
+# functions that are documented, but have no documentation for their parameters 
+# or return value. If set to NO (the default) doxygen will only warn about 
+# wrong or incomplete parameter documentation, but not about the absence of 
+# documentation.
+
+WARN_NO_PARAMDOC       = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that 
+# doxygen can produce. The string should contain the $file, $line, and $text 
+# tags, which will be replaced by the file and line number from which the 
+# warning originated and the warning text. Optionally the format may contain 
+# $version, which will be replaced by the version of the file (if it could 
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning 
+# and error messages should be written. If left blank the output is written 
+# to stderr.
+
+WARN_LOGFILE           = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain 
+# documented source files. You may enter file names like "myfile.cpp" or 
+# directories like "/usr/src/myproject". Separate the files or directories 
+# with spaces.
+
+INPUT                  = libmaple/ \
+                         wirish/
+
+# This tag can be used to specify the character encoding of the source files 
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
+# also the default input encoding. Doxygen uses libiconv (or the iconv built 
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for 
+# the list of possible encodings.
+
+INPUT_ENCODING         = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the 
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank the following patterns are tested: 
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+
+FILE_PATTERNS          = *.c \
+                         *.cpp \
+                         *.h
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
+# should be searched for input files as well. Possible values are YES and NO. 
+# If left blank NO is used.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should 
+# excluded from the INPUT source files. This way you can easily exclude a 
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE                = 
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
+# directories that are symbolic links (a Unix filesystem feature) are excluded 
+# from the input.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the 
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
+# certain files from those directories. Note that the wildcards are matched 
+# against the file with absolute path, so to exclude all test directories 
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       = 
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
+# (namespaces, classes, functions, etc.) that should be excluded from the 
+# output. The symbol name can be a fully qualified name, a word, or if the 
+# wildcard * is used, a substring. Examples: ANamespace, AClass, 
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS        = 
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or 
+# directories that contain example code fragments that are included (see 
+# the \include command).
+
+EXAMPLE_PATH           = 
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank all files are included.
+
+EXAMPLE_PATTERNS       = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
+# searched for input files to be used with the \include or \dontinclude 
+# commands irrespective of the value of the RECURSIVE tag. 
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or 
+# directories that contain image that are included in the documentation (see 
+# the \image command).
+
+IMAGE_PATH             = 
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should 
+# invoke to filter for each input file. Doxygen will invoke the filter program 
+# by executing (via popen()) the command <filter> <input-file>, where <filter> 
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
+# input file. Doxygen will then use the output that the filter program writes 
+# to standard output.  If FILTER_PATTERNS is specified, this tag will be 
+# ignored.
+
+INPUT_FILTER           = 
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern 
+# basis.  Doxygen will compare the file name with each pattern and apply the 
+# filter if there is a match.  The filters are a list of the form: 
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further 
+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER 
+# is applied to all files.
+
+FILTER_PATTERNS        = 
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
+# INPUT_FILTER) will be used to filter the input files when producing source 
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES    = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
+# be generated. Documented entities will be cross-referenced with these sources. 
+# Note: To get rid of all source code in the generated output, make sure also 
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER         = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body 
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
+# doxygen to hide any special comment blocks from generated source code 
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES 
+# then for each documented function all documented 
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES 
+# then for each documented function all documented entities 
+# called/used by that function will be listed.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) 
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from 
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will 
+# link to the source code.  Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code 
+# will point to the HTML generated by the htags(1) tool instead of doxygen 
+# built-in source browser. The htags tool is part of GNU's global source 
+# tagging system (see http://www.gnu.org/software/global/global.html). You 
+# will need version 4.8.6 or higher.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
+# will generate a verbatim copy of the header file for each class for 
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
+# of all compounds will be generated. Enable this if the project 
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX     = YES
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all 
+# classes will be put under the same header in the alphabetical index. 
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX          = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
+# generate HTML output.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard header.
+
+HTML_HEADER            = 
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard footer.
+
+HTML_FOOTER            = 
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
+# style sheet that is used by each HTML page. It can be used to 
+# fine-tune the look of the HTML output. If the tag is left blank doxygen 
+# will generate a default style sheet. Note that doxygen will try to copy 
+# the style sheet file to the HTML output directory, so don't put your own 
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET        = 
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. 
+# Doxygen will adjust the colors in the stylesheet and background images 
+# according to this color. Hue is specified as an angle on a colorwheel, 
+# see http://en.wikipedia.org/wiki/Hue for more information. 
+# For instance the value 0 represents red, 60 is yellow, 120 is green, 
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. 
+# The allowed range is 0 to 359.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of 
+# the colors in the HTML output. For a value of 0 the output will use 
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to 
+# the luminance component of the colors in the HTML output. Values below 
+# 100 gradually make the output lighter, whereas values above 100 make 
+# the output darker. The value divided by 100 is the actual gamma applied, 
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, 
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML 
+# page will contain the date and time when the page was generated. Setting 
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP         = YES
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
+# files or namespaces will be aligned in HTML using tables. If set to 
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS     = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
+# documentation will contain sections that can be hidden and shown after the 
+# page has loaded. For this to work a browser that supports 
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files 
+# will be generated that can be used as input for Apple's Xcode 3 
+# integrated development environment, introduced with OSX 10.5 (Leopard). 
+# To create a documentation set, doxygen will generate a Makefile in the 
+# HTML output directory. Running make will produce the docset in that 
+# directory and running "make install" will install the docset in 
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find 
+# it at startup. 
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html 
+# for more information.
+
+GENERATE_DOCSET        = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the 
+# feed. A documentation feed provides an umbrella under which multiple 
+# documentation sets from a single provider (such as a company or product suite) 
+# can be grouped.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that 
+# should uniquely identify the documentation set bundle. This should be a 
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen 
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify 
+# the documentation publisher. This should be a reverse domain-name style 
+# string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
+# will be generated that can be used as input for tools like the 
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP      = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
+# be used to specify the file name of the resulting .chm file. You 
+# can add a path in front of the file if the result should not be 
+# written to the html output directory.
+
+CHM_FILE               = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
+# be used to specify the location (absolute path including file name) of 
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION           = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
+# controls if a separate .chi index file is generated (YES) or that 
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI           = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING 
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file 
+# content.
+
+CHM_INDEX_ENCODING     = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
+# controls whether a binary table of contents is generated (YES) or a 
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members 
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and 
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated 
+# that can be used as input for Qt's qhelpgenerator to generate a 
+# Qt Compressed Help (.qch) of the generated HTML documentation.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can 
+# be used to specify the file name of the resulting .qch file. 
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE               = 
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating 
+# Qt Help Project output. For more information please see 
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating 
+# Qt Help Project output. For more information please see 
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to 
+# add. For more information please see 
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME   = 
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the 
+# custom filter to add. For more information please see 
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters"> 
+# Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS  = 
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this 
+# project's 
+# filter section matches. 
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes"> 
+# Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS  = 
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can 
+# be used to specify the location of Qt's qhelpgenerator. 
+# If non-empty doxygen will try to run qhelpgenerator on the generated 
+# .qhp file.
+
+QHG_LOCATION           = 
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files  
+# will be generated, which together with the HTML files, form an Eclipse help 
+# plugin. To install this plugin and make it available under the help contents 
+# menu in Eclipse, the contents of the directory containing the HTML and XML 
+# files needs to be copied into the plugins directory of eclipse. The name of 
+# the directory within the plugins directory should be the same as 
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before 
+# the help appears.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin 
+# the directory name containing the HTML and XML files should also have 
+# this name.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
+# top of each HTML page. The value NO (the default) enables the index and 
+# the value YES disables it.
+
+DISABLE_INDEX          = NO
+
+# This tag can be used to set the number of enum values (range [1..20]) 
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index 
+# structure should be generated to display hierarchical information. 
+# If the tag value is set to YES, a side panel will be generated 
+# containing a tree-like index structure (just like the one that 
+# is generated for HTML Help). For this to work a browser that supports 
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). 
+# Windows users are probably better off using the HTML help feature.
+
+GENERATE_TREEVIEW      = NO
+
+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, 
+# and Class Hierarchy pages using a tree view instead of an ordered list.
+
+USE_INLINE_TREES       = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
+# used to set the initial width (in pixels) of the frame in which the tree 
+# is shown.
+
+TREEVIEW_WIDTH         = 250
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open 
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# Use this tag to change the font size of Latex formulas included 
+# as images in the HTML documentation. The default is 10. Note that 
+# when you change the font size after a successful doxygen run you need 
+# to manually remove any form_*.png images from the HTML output directory 
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE       = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images 
+# generated for formulas are transparent PNGs. Transparent PNGs are 
+# not supported properly for IE 6.0, but are supported on all modern browsers. 
+# Note that when changing this option you need to delete any form_*.png files 
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT    = YES
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box 
+# for the HTML output. The underlying search engine uses javascript 
+# and DHTML and should work on any modern browser. Note that when using 
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets 
+# (GENERATE_DOCSET) there is already a search function so this one should 
+# typically be disabled. For large projects the javascript based search engine 
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be 
+# implemented using a PHP enabled web server instead of at the web client 
+# using Javascript. Doxygen will generate the search PHP script and index 
+# file to put on the web server. The advantage of the server 
+# based approach is that it scales better to large projects and allows 
+# full text search. The disadvances is that it is more difficult to setup 
+# and does not have live searching capabilities.
+
+SERVER_BASED_SEARCH    = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
+# generate Latex output.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
+# invoked. If left blank `latex' will be used as the default command name. 
+# Note that when enabling USE_PDFLATEX this option is only used for 
+# generating bitmaps for formulas in the HTML output, but not in the 
+# Makefile that is written to the output directory.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
+# generate index for LaTeX. If left blank `makeindex' will be used as the 
+# default command name.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
+# LaTeX documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used 
+# by the printer. Possible values are: a4, a4wide, letter, legal and 
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE             = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES         = 
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
+# the generated latex document. The header should contain everything until 
+# the first chapter. If it is left blank doxygen will generate a 
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER           = 
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
+# contain links (just like the HTML output) instead of page references 
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS         = YES
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
+# plain latex in the generated Makefile. Set this option to YES to get a 
+# higher quality PDF documentation.
+
+USE_PDFLATEX           = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
+# command to the generated LaTeX files. This will instruct LaTeX to keep 
+# running if errors occur, instead of asking the user for help. 
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE        = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
+# include the index chapters (such as File Index, Compound Index, etc.) 
+# in the output.
+
+LATEX_HIDE_INDICES     = NO
+
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include 
+# source code with syntax highlighting in the LaTeX output. 
+# Note that which sources are shown also depends on other settings 
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE      = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
+# The RTF output is optimized for Word 97 and may not look very pretty with 
+# other RTF readers or editors.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
+# RTF documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
+# will contain hyperlink fields. The RTF file will 
+# contain links (just like the HTML output) instead of page references. 
+# This makes the output suitable for online browsing using WORD or other 
+# programs which support those fields. 
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's 
+# config file, i.e. a series of assignments. You only have to provide 
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE    = 
+
+# Set optional variables used in the generation of an rtf document. 
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE    = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
+# generate man pages
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to 
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION          = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
+# then it will generate one additional man file for each entity 
+# documented in the real man page(s). These additional files 
+# only source the real man page, but without them the man command 
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will 
+# generate an XML file that captures the structure of 
+# the code including all documentation.
+
+GENERATE_XML           = YES
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT             = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_SCHEMA             = 
+
+# The XML_DTD tag can be used to specify an XML DTD, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_DTD                = 
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
+# dump the program listings (including syntax highlighting 
+# and cross-referencing information) to the XML output. Note that 
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
+# generate an AutoGen Definitions (see autogen.sf.net) file 
+# that captures the structure of the code including all 
+# documentation. Note that this feature is still experimental 
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
+# generate a Perl module file that captures the structure of 
+# the code including all documentation. Note that this 
+# feature is still experimental and incomplete at the 
+# moment.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
+# nicely formatted so it can be parsed by a human reader.  This is useful 
+# if you want to understand what is going on.  On the other hand, if this 
+# tag is set to NO the size of the Perl module output will be much smaller 
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file 
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
+# This is useful so different doxyrules.make files included by the same 
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX = 
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
+# evaluate all C-preprocessor directives found in the sources and include 
+# files.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
+# names in the source code. If set to NO (the default) only conditional 
+# compilation will be performed. Macro expansion can be done in a controlled 
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
+# then the macro expansion is limited to the macros specified with the 
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that 
+# contain include files that are not input files but should be processed by 
+# the preprocessor.
+
+INCLUDE_PATH           = 
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
+# patterns (like *.h and *.hpp) to filter out the header-files in the 
+# directories. If left blank, the patterns specified with FILE_PATTERNS will 
+# be used.
+
+INCLUDE_FILE_PATTERNS  = 
+
+# The PREDEFINED tag can be used to specify one or more macro names that 
+# are defined before the preprocessor is started (similar to the -D option of 
+# gcc). The argument of the tag is a list of macros of the form: name 
+# or name=definition (no spaces). If the definition and the = are 
+# omitted =1 is assumed. To prevent a macro definition from being 
+# undefined via #undef or recursively expanded use the := operator 
+# instead of the = operator.
+
+PREDEFINED             = 
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
+# this tag can be used to specify a list of macro names that should be expanded. 
+# The macro definition that is found in the sources will be used. 
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED      = 
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
+# doxygen's preprocessor will remove all function-like macros that are alone 
+# on a line, have an all uppercase name, and do not end with a semicolon. Such 
+# function macros are typically used for boiler-plate code, and will confuse 
+# the parser if not removed.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles. 
+# Optionally an initial location of the external documentation 
+# can be added for each tagfile. The format of a tag file without 
+# this location is as follows: 
+#   TAGFILES = file1 file2 ... 
+# Adding location for the tag files is done as follows: 
+#   TAGFILES = file1=loc1 "file2 = loc2" ... 
+# where "loc1" and "loc2" can be relative or absolute paths or 
+# URLs. If a location is present for each tag, the installdox tool 
+# does not have to be run to correct the links. 
+# Note that each tag file must have a unique name 
+# (where the name does NOT include the path) 
+# If a tag file is not located in the directory in which doxygen 
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES               = 
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE       = 
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
+# in the class index. If set to NO only the inherited external classes 
+# will be listed.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
+# in the modules index. If set to NO, only the current project's groups will 
+# be listed.
+
+EXTERNAL_GROUPS        = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script 
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base 
+# or super classes. Setting the tag to NO turns the diagrams off. Note that 
+# this option is superseded by the HAVE_DOT option below. This is only a 
+# fallback. It is recommended to install and use dot, since it yields more 
+# powerful graphs.
+
+CLASS_DIAGRAMS         = YES
+
+# You can define message sequence charts within doxygen comments using the \msc 
+# command. Doxygen will then run the mscgen tool (see 
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the 
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where 
+# the mscgen tool resides. If left empty the tool is assumed to be found in the 
+# default search path.
+
+MSCGEN_PATH            = 
+
+# If set to YES, the inheritance and collaboration graphs will hide 
+# inheritance and usage relations if the target is undocumented 
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
+# available from the path. This tool is part of Graphviz, a graph visualization 
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT               = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is 
+# allowed to run in parallel. When set to 0 (the default) doxygen will 
+# base this on the number of processors available in the system. You can set it 
+# explicitly to a value larger than 0 to get control over the balance 
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS        = 0
+
+# By default doxygen will write a font called FreeSans.ttf to the output 
+# directory and reference it in all dot files that doxygen generates. This 
+# font does not include all possible unicode characters however, so when you need 
+# these (or just want a differently looking font) you can specify the font name 
+# using DOT_FONTNAME. You need need to make sure dot is able to find the font, 
+# which can be done by putting it in a standard location or by setting the 
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
+# containing the font.
+
+DOT_FONTNAME           = FreeSans.ttf
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
+# The default size is 10pt.
+
+DOT_FONTSIZE           = 10
+
+# By default doxygen will tell dot to use the output directory to look for the 
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a 
+# different font using DOT_FONTNAME you can set the path where dot 
+# can find it using this tag.
+
+DOT_FONTPATH           = 
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect inheritance relations. Setting this tag to YES will force the 
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect implementation dependencies (inheritance, containment, and 
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH    = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS           = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
+# collaboration diagrams in a style similar to the OMG's Unified Modeling 
+# Language.
+
+UML_LOOK               = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the 
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
+# tags are set to YES then doxygen will generate a graph for each documented 
+# file showing the direct and indirect include dependencies of the file with 
+# other documented files.
+
+INCLUDE_GRAPH          = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
+# documented header file showing the documented files that directly or 
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH      = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then 
+# doxygen will generate a call dependency graph for every global function 
+# or class method. Note that enabling this option will significantly increase 
+# the time of a run. So in most cases it will be better to enable call graphs 
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH             = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then 
+# doxygen will generate a caller dependency graph for every global function 
+# or class method. Note that enabling this option will significantly increase 
+# the time of a run. So in most cases it will be better to enable caller 
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH           = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY    = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES 
+# then doxygen will show the dependencies a directory has on other directories 
+# in a graphical way. The dependency relations are determined by the #include 
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH        = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
+# generated by dot. Possible values are png, jpg, or gif 
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT       = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be 
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH               = 
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that 
+# contain dot files that are included in the documentation (see the 
+# \dotfile command).
+
+DOTFILE_DIRS           = 
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of 
+# nodes that will be shown in the graph. If the number of nodes in a graph 
+# becomes larger than this value, doxygen will truncate the graph, which is 
+# visualized by representing a node as a red box. Note that doxygen if the 
+# number of direct children of the root node in a graph is already larger than 
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note 
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES    = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
+# graphs generated by dot. A depth value of 3 means that only nodes reachable 
+# from the root by following a path via at most 3 edges will be shown. Nodes 
+# that lay further from the root node will be omitted. Note that setting this 
+# option to 1 or 2 may greatly reduce the computation time needed for large 
+# code bases. Also note that the size of a graph can be further restricted by 
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
+# background. This is disabled by default, because dot on Windows does not 
+# seem to support this out of the box. Warning: Depending on the platform used, 
+# enabling this option may lead to badly anti-aliased labels on the edges of 
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT        = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output 
+# files in one run (i.e. multiple -o and -T options on the command line). This 
+# makes dot run faster, but since only newer versions of dot (>1.8.10) 
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS      = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
+# generate a legend page explaining the meaning of the various boxes and 
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
+# remove the intermediate dot files that are used to generate 
+# the various graphs.
+
+DOT_CLEANUP            = YES
diff --git a/README b/README
index 8556dd2..174f55a 100644
--- a/README
+++ b/README
@@ -1,22 +1,36 @@
-This directory contains the Sphinx documentation for libmaple.  You
-can generate HTML documentation using the Makefile if you have make,
-or using make.bat from Windows.
+This directory contains the Sphinx documentation for libmaple, as well
+as a Doxygen configuration file; we turn Doxygen XML output into
+Sphinx documentation.  You can generate HTML documentation using the
+Makefile if you have make, or using make.bat from Windows.
 
-For the impatient, you can build the HTML docs with (on Unix):
+You need a recent-ish version of doxygen in your PATH:
+
+    http://www.stack.nl/~dimitri/doxygen/download.html#latestsrc
+
+For the Doxygen-to-Sphinx bridge, we rely on a project called Breathe,
+by Michael Jones.  You must clone the breathe repository and set an
+environment variable BREATHE_HOME to be able to build the
+documentation.  Something like this on bash:
+
+    $ git clone http://github.com/michaeljones/breathe.git
+    $ export BREATHE_HOME /path/to/breathe/repo/
+
+You can now build the HTML docs with (on Unix):
 
     $ sudo easy_install -U Sphinx
     $ make html
 
-Which will produce HTML documentation in build/html.
+Which will produce Doxygen documentation in doxygen/xml, and HTML
+documentation (this is what you want to look at) in build/html.
 
 All of the documentation itself lives in source/.  The directory
 source/_static is for static content like style sheets;
-source/_templates contains Sphinx templates.
+source/_templates contains Sphinx templates (or, it would if we had
+any).
 
-The documentation is written in reStructuredText (reST); it's a Python
-thing that they use to produce the docs at python.org (which are
-beautiful, if you've never seen them).  You can read more about Sphinx
-here:
+The docs are written in reStructuredText (reST); it's a Python thing
+that they use to produce the docs at python.org (which are beautiful,
+if you've never seen them).  You can read more about Sphinx here:
 
     http://sphinx.pocoo.org/tutorial.html
 
@@ -24,5 +38,8 @@ Specific information on documenting C and C++ is available here:
 
     http://sphinx.pocoo.org/domains.html
 
-The file source/conf.py is an autogenerated configuration file; you
-can read it yourself.
+You can view the reST source for any generated page of documentation
+by clicking the "Show Source" link in the sidebar.
+
+The file source/conf.py is the Sphinx configuration file; you can go
+read it for more information about our setup.
diff --git a/source/adc.rst b/source/adc.rst
index 17c672d..4e118aa 100644
--- a/source/adc.rst
+++ b/source/adc.rst
@@ -4,4 +4,72 @@
  ADC
 =====
 
-Stub.
+Analog-Digital Conversion is the process of reading a physical voltage
+as a number. The Maple has a large number of pins which are capable of
+taking 12-bit ADC measurements, which means that voltages from ground
+to +3.3v are read as numbers from 0 to 4095; this corresponds to a
+theoretical sensitivity of just under 1 millivolt. In reality, a
+number of factors introduce noise and bias into this reading and a
+number of techniques must be used to get good precision and accuracy.
+
+.. compound::
+
+   The header pins with ADC functionality (marked as "AIN" on the
+   silkscreen) are:
+
+     D0, D1, D2, D3, D10, D11, D12, D13, D15, D16, D17, D18, D19, D20, D27, D28
+
+.. contents:: Contents
+   :local:
+
+.. _adc-noise-bias:
+
+Noise and Bias
+--------------
+
+The biggest issues with analog-digital conversion are noise and bias.
+With the Maple, we have tried to isolate the ADC pins and traces from
+strong noise sources but there are always trade--offs between noise,
+additional functionality, cost, and package size.
+
+The 6 ADC pins in a bank (D15--D20) generally have the least
+noise and should be used for fine measurements.  If the input voltage
+changes relatively slowly, a number of samples can be taken in
+succession and averaged together, or the same voltage can even be
+sampled by multiple ADC pins at the same time.
+
+An important factor when taking a voltage reading is the reference
+voltages that the sample is being compared against. In the case of the
+Maple, the high reference is |vcc| and the low reference is ground.
+This means that noise or fluctuations on either |vcc| or ground will
+affect the measurement. It also means that the voltage you are trying
+to sample must be between ground and 3.3V. In the case of a variable
+reading, it is best if the voltage varies over the entire range of
+0--3.3V; otherwise, only a fraction of the sensitivity is being
+leveraged.  Resistor dividers and constant voltage diodes are basic
+tools which can help bring a given voltage signal into the appropriate
+range; opamps and other powered components can also be used.
+
+.. _adc-function-reference:
+
+Function Reference
+------------------
+
+.. TODO function reference (figure out Doxygen first)
+
+.. _adc-recommended-reading:
+
+Recommended Reading
+-------------------
+
+* `Wikipedia article on Analog-to-digital converter <http://en.wikipedia.org/wiki/Analog-to-digital_converter>`_
+* `Arduino Analog Input Tutorial <http://arduino.cc/en/Tutorial/AnalogInputPins>`_
+* STMicro documentation for STM32F103RB microcontroller:
+
+  * `All <http://www.st.com/mcu/devicedocs-STM32F103RB-110.html>`_
+  * `Datasheet (pdf) <http://www.st.com/stonline/products/literature/ds/13587.pdf>`_
+  * `Reference Manual (pdf) <http://www.st.com/stonline/products/literature/rm/13902.pdf>`_
+  * `Application Note on ADC Modes (pdf) <http://www.st.com/stonline/products/literature/an/16840.pdf>`_
+  * `Application Note on ADC Oversampling (pdf) <http://www.st.com/stonline/products/literature/an/14183.pdf>`_
+
+
diff --git a/source/bootloader.rst b/source/bootloader.rst
index 9280c68..c4c5da2 100644
--- a/source/bootloader.rst
+++ b/source/bootloader.rst
@@ -15,6 +15,9 @@ Flash memory and only runs when the chip is reset).
 
 **Visit the github development project**: http://github.com/leaflabs/maple-bootloader
 
+.. contents:: Contents
+   :local:
+
 Bootloader Schemes Explained!
 -----------------------------
 
diff --git a/source/compatibility.rst b/source/compatibility.rst
index aeed36b..6166ec5 100644
--- a/source/compatibility.rst
+++ b/source/compatibility.rst
@@ -1,7 +1,136 @@
+.. highlight:: cpp
+
 .. _compatibility:
 
 =============================
  Maple-Arduino Compatibility
 =============================
 
+.. contents:: Contents
+   :local:
+
+Overview
+--------
+
+The biggest difference between the Maple and most Arduino boards is
+that the Maple uses a 32-bit ARM Cortex-M3 architecture chip while the
+Arduinos have 8-bit Atmel AVR chips. The different instruction set
+means that machine code (executable binary programs) is incompatible
+between the two, and a different compiler (actually just a different
+version of `gcc <http://gcc.gnu.org/>`_) is required. The compiler for
+the regular Arduino IDE is the popular :command:`avr-gcc` package; the
+compiler for the Maple version of the IDE is CodeSourcery's edition of
+gcc for the ARM EABI target (:command:`arm-non-eabi-gcc`).
+
+The bitwidth of the processor means that the Maple can process 32-bit
+operations (like adding two 32-bit integers) in a single instruction,
+while an Arduino processor would have to split up large operations
+into several smaller ones. In a lot of cases 8-bit operations are
+plenty (integers 0-255, single characters of text, etc.), but if
+you're dealing with higher resolution data, the speed up could be
+significant. A trade-off is that code could be larger as well; program
+instructions and memory locations can be up to 32-bits each, which in
+the worst case would quadruple program size. In reality, the removal
+of extra instructions and fancy packing together of simple
+instructions means that programs aren't much larger (or are even
+smaller).
+
+Header Numbering and Incompatibilities
+--------------------------------------
+
+The numbering of headers is different; on the Maple each GPIO has a
+unique number: D0, D1, D2, all the way up to D37 (actually, there are
+:ref:`a few more <jtag>`...). On the Arduino, the analog pins are
+numbered separately (A0-A5) from the digital pins (D0\ -D13).
+
+The incompatible hardware differences are:
+
+* |i2c| port: on most Arduinos, the |i2c| port is Analog Input
+  4 (SDA) and Analog Input 5 (SCL); on the Maple, |i2c| port 1 is D5
+  (SCL) and D9 (SDA), and |i2c| port 2 is D29 (SCL) and D30 (SDA).
+
+  It should be possible to skywire, sacrificing signal quality (due to
+  increased capacitance). Alternatively, |i2c| can be bit-banged
+  reasonably well in software. This peripheral could potentially be
+  rerouted internally, but we haven't looked into it.
+
+* :ref:`PWM <pwm>` on D10: all the other standard Arduino PWM headers have PWM
+  functionality on the Maple (D2,D3,D6,D9,D11), but not D10. We did
+  our best! It may be possible to reroute this peripheral internally
+  using low level configuration, but we haven't looked in to it.
+
+* No External Voltage Reference: The Arduino has an Aref pin which
+  allows the use of an external ADC voltage reference; the Maple has
+  an extra GPIO pin (14) with PWM capability in this spot, and does
+  not allow an external voltage reference to be configured.
+
+* EEPROM: the Maple does not have any internal EEPROM. This
+  functionality can be emulated with regular persistent flash memory,
+  or with an external EEPROM chip.
+
+* ISP Programming: the Maple does not use an ISP/ICSP bus for
+  debugging; it uses :ref:`JTAG <jtag>`.
+
+
+Software Language/Library Changes
+---------------------------------
+
+With :ref:`one notable exception <language-no-word>`, the entire
+Arduino language is supported.  However, there are some subtle
+differences, most of which are improvements:
+
+* 32-bit integers: many standard functions either expect or return
+  full 32-bit (4 byte) integer values instead of the regular 16-bit (2
+  byte) Arduino values.
+
+* `pinMode()`_ types: any :ref:`GPIO <gpio>` (including analog pins)
+  can be configured into one of the following modes with a single call
+  to `pinMode()`_: ``OUTPUT``, ``OUTPUT_OPEN_DRAIN``,
+  ``INPUT_FLOATING``, ``INPUT_PULLUP``,
+  ``INPUT_PULLDOWN``. Additionally, the PWM and Analog Input pins can
+  be configured as ``INPUT_ANALOG`` and ``PWM`` respectively. See the
+  :ref:`GPIO documentation <gpio>` for more information.
+
+  .. TODO: reference libmaple docs above when they're done
+
+* Serial1 syntax: like the `Arduino Mega
+  <http://arduino.cc/en/Main/ArduinoBoardMega>`_, the Maple has
+  multiple USART ports.  By default, Serial is not mapped to any of
+  them, use ``Serial1`` through ``Serial3`` instead.
+
+  .. TODO: reference libmaple docs for Serial[n] above when they're done
+
+* 16-bit :ref:`PWM <pwm>`: Arduino boards support 8-bit PWM, which
+  means that calls to `analogWrite()`_ take values between 0 (always
+  off) and 255 (always on).  The Maple supports 16-bit PWM, so the
+  corresponding values should be between 0 (always off) and 65535
+  (always on).
+
+* 12-bit :ref:`ADC <adc>`: Arduino boards support 10-bit ADC, which
+  means that calls to `analogRead()`_ will return values between 0 and
+  1023.  The Maple supports 12-bit ADC, so the same call will instead
+  return values between 0 and 4095.
+
+
+.. class:: ported-feature
+
+I am supported!
+
+This should be ordinary
+
+.. class:: non-ported-feature
+
+I can't do it :(
+
+Also ordinary
+
+.. class:: partly-ported-feature
+
+I sorta work
+
+And I am also ordinary
+
 Stub.
+
+(not finished)
+
diff --git a/source/conf.py b/source/conf.py
index 5fcb939..26147fd 100644
--- a/source/conf.py
+++ b/source/conf.py
@@ -17,7 +17,11 @@ import sys, os
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+#
+# We rely on Michael Jones's breathe as a Doxygen-to-Sphinx bridge.
+# See libmaple/docs/README for information on obtaining it and letting
+# Sphinx know where it is.
+sys.path.append(os.environ['BREATHE_HOME'])
 
 # -- General configuration ----------------------------------------------------
 
@@ -29,7 +33,7 @@ import sys, os
 # ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
               'sphinx.ext.intersphinx', 'sphinx.ext.todo',
-              'sphinx.ext.coverage']
+              'sphinx.ext.coverage', 'breathe']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -68,12 +72,16 @@ release = '0.0.7'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['epilog.rst']
+exclude_patterns = ['epilog.rst', 'prolog.rst']
 
 # Included at the end of every source file that is read.
 with open('epilog.rst', 'r') as ep:
     rst_epilog = ep.read()
 
+# Included at the beginning of every source file that is read.
+with open('prolog.rst', 'r') as pr:
+    rst_prolog = pr.read()
+
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
 #default_role = None
@@ -229,3 +237,11 @@ man_pages = [
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'http://docs.python.org/': None}
+
+
+# -- Options for breathe integration ------------------------------------------
+
+breathe_projects = {'libmaple' : os.path.join(os.environ['LIB_MAPLE_HOME'],
+                                              'docs', 'doxygen', 'xml')}
+
+breathe_default_project = 'libmaple'
diff --git a/source/epilog.rst b/source/epilog.rst
index 0e430c8..7805362 100644
--- a/source/epilog.rst
+++ b/source/epilog.rst
@@ -4,5 +4,56 @@
 .. Common URL references
 .. _forum: http://forums.leaflabs.com
 .. _contact: http://leaflabs.com/contact/
+
+
+.. Arduino built-in functions
 .. _setup(): http://arduino.cc/en/Reference/Setup
 .. _loop(): http://arduino.cc/en/Reference/Loop
+
+.. _pinMode(): http://arduino.cc/en/Reference/PinMode
+.. _digitalWrite(): http://arduino.cc/en/Reference/DigitalWrite
+.. _digitalRead(): http://arduino.cc/en/Reference/DigitalRead
+
+.. _analogReference(): http://arduino.cc/en/Reference/AnalogReference
+.. _analogRead(): http://arduino.cc/en/Reference/AnalogRead
+.. _analogWrite(): http://arduino.cc/en/Reference/AnalogWrite
+
+.. _tone(): http://arduino.cc/en/Reference/Tone
+.. _noTone(): http://arduino.cc/en/Reference/NoTone
+.. _shiftOut(): http://arduino.cc/en/Reference/ShiftOut
+.. _pulseIn(): http://arduino.cc/en/Reference/PulseIn
+
+.. _millis(): http://arduino.cc/en/Reference/Millis
+.. _micros(): http://arduino.cc/en/Reference/Micros
+.. _delay(): http://arduino.cc/en/Reference/Delay
+.. _delayMicroseconds(): http://arduino.cc/en/Reference/DelayMicroseconds
+
+.. _min(): http://arduino.cc/en/Reference/Min
+.. _max(): http://arduino.cc/en/Reference/Max
+.. _abs(): http://arduino.cc/en/Reference/Abs
+.. _constrain(): http://arduino.cc/en/Reference/Constrain
+
+.. _map(): http://arduino.cc/en/Reference/Map
+.. _pow(): http://arduino.cc/en/Reference/Pow
+.. _sqrt(): http://arduino.cc/en/Reference/Sqrt
+
+.. _sin(): http://arduino.cc/en/Reference/Sin
+.. _cos(): http://arduino.cc/en/Reference/Cos
+.. _tan(): http://arduino.cc/en/Reference/Tan
+
+.. _randomSeed(): http://arduino.cc/en/Reference/RandomSeed
+.. _random(): http://arduino.cc/en/Reference/Random
+
+.. _lowByte(): http://arduino.cc/en/Reference/LowByte
+.. _highByte(): http://arduino.cc/en/Reference/HighByte
+.. _bitRead(): http://arduino.cc/en/Reference/BitRead
+.. _bitWrite(): http://arduino.cc/en/Reference/BitWrite
+.. _bitSet(): http://arduino.cc/en/Reference/BitSet
+.. _bitClear(): http://arduino.cc/en/Reference/BitClear
+.. _bit(): http://arduino.cc/en/Reference/Bit
+
+.. _attachInterrupt(): http://arduino.cc/en/Reference/AttachInterrupt
+.. _detachInterrupt(): http://arduino.cc/en/Reference/DetachInterrupt
+
+.. _interrupts(): http://arduino.cc/en/Reference/Interrupts
+.. _noInterrupts(): http://arduino.cc/en/Reference/NoInterrupts
diff --git a/source/errata.rst b/source/errata.rst
index b702bd1..09b2ad1 100644
--- a/source/errata.rst
+++ b/source/errata.rst
@@ -4,4 +4,15 @@
  Errata
 ========
 
+This page is a collection of known issues and warnings for each
+revision of the Maple board. The failure modes aren't design errors,
+but are easy ways to break or damage your board permanently. For a
+list of differences between the Maple and Arduinos, see the page on
+:ref:`compatibility <compatibility>`.
+
+.. contents:: Contents
+   :local:
+
 Stub.
+
+(not finished)
diff --git a/source/gpio.rst b/source/gpio.rst
index f608a61..2567221 100644
--- a/source/gpio.rst
+++ b/source/gpio.rst
@@ -4,4 +4,91 @@
  GPIO
 ======
 
-Stub.
+The Maple features 38 ready-to-use general purpose input/output (GPIO)
+pins for digital input/output, numbered D0 through D37.  These numbers
+correspond to the numeric values next to each header on the Maple
+silkscreen.
+
+Many of these pins may additionally be used for special features or
+peripheral functions.  This page documents those capabilities, by pin.
+
+The current and voltage limitations have not been copied over from the
+STM32 datasheet (see the :ref:`Recommended Reading
+<gpio-recommended-reading>` for a link).  In particular, a number of
+GPIO pins are 5v tolerant (which means that applying 5v to a pin and
+reading it as input or allowing it to drain to ground will not damage
+that pin), while some are not.
+
+.. contents:: Contents
+   :local:
+
+Pin Mapping Mega Table
+----------------------
+
+This huge reference table shows the available functionality on every
+GPIO pin, by peripheral type. The "STM32" column refers to the port
+and number that the header is connected to on the microcontroller.
+The "5v?" column documents whether or not the pin is 5v tolerant (see
+above).
+
+.. csv-table::
+   :header: "Pin", "STM32", ":ref:`ADC <adc>`", ":ref:`Timer <timers>`", ":ref:`I2C <i2c>`", ":ref:`UART <usart>`", ":ref:`SPI <spi>`", "5v?"
+
+   "D0",  "PA3",  "ADC3", "TIM2_CH4",     "-",         "USART2_RX",  "-",         "No"
+   "D1",  "PA2",  "ADC2", "TIM2_CH3",     "-",         "USART2_TX",  "-",         "No"
+   "D2",  "PA0",  "ADC0", "TIM2_CH1_ETR", "-",         "USART2_CTS", "-",         "No"
+   "D3",  "PA1",  "ADC1", "TIM2_CH2",     "-",         "USART2_RTS", "-",         "No"
+   "D4",  "PB5",  "-",    "-",            "ISC1_SMBA", "-",          "-",         "No"
+   "D5",  "PB6",  "-",    "TIM4_CH1",     "I2C1_SCL",  "-",          "-",         "Yes"
+   "D6",  "PA8",  "-",    "TIM1_CH1",     "-",         "USART1_CK",  "-",         "Yes"
+   "D7",  "PA9",  "-",    "TIM1_CH2",     "-",         "USART1_TX",  "-",         "Yes"
+   "D8",  "PA10", "-",    "TIM1_CH3",     "-",         "USART1_RX",  "-",         "Yes"
+   "D9",  "PB7",  "-",    "TIM4_CH2",     "I2C1_SDA",  "-",          "-",         "Yes"
+   "D10", "PA4",  "ADC4", "-",            "-",         "USART2_CK",  "SPI1_NSS",  "No"
+   "D11", "PA7",  "ADC7", "TIM3_CH2",     "-",         "-",          "SPI1_MOSI", "No"
+   "D12", "PA6",  "ADC6", "TIM3_CH1",        -       -       SPI1_MISO       No
+   D13  PA5     ADC5    -       -       -       SPI1_SCK        No
+   D14  PB8     -       TIM4_CH3        -       -       -       Yes
+
+   Analog header
+
+   D15  PC0     ADC10   -       -       -       -       No
+   D16  PC1     ADC11   -       -       -       -       No
+   D17  PC2     ADC12   -       -       -       -       No
+   D18  PC3     ADC13   -       -       -       -       No
+   D19  PC4     ADC14   -       -       -       -       No
+   D20  PC5     ADC15   -       -       -       -       No
+
+   External header
+
+   D21  PC13    -       -       -       -       -       No
+   D22  PC14    -       -       -       -       -       No
+   D23  PC15    -       -       -       -       -       No
+   D24  PB9     -       TIM4_CH4        -       -       -       Yes
+   D25  PD2     -       TIM3_ETR        -       -       -       Yes
+   D26  PC10    -       -       -       -       -       Yes
+   D27  PB0     ADC8    TIM3_CH3        -       -       -       No
+   D28  PB1     ADC9    TIM3_CH4        -       -       -       No
+   D29  PB10    -       -       I2C2_SCL        USART3_TX       -       Yes
+   D30  PB11    -       -       I2C2_SDA        USART3_RX       -       Yes
+   D31  PB12    -       TIM1_BKIN       I2C2_SMBAL      USART3_CK       SPI2_NSS        Yes
+   D32  PB13    -       TIM1_CH1N       -       USART3_CTS      SPI2_SCK        Yes
+   D33  PB14    -       TIM1_CH2N       -       USART3_RTS      SPI2_MISO       Yes
+   D34  PB15    -       TIM1_CH3N       -       -       SPI2_MOSI       Yes
+   D35  PC6     -       -       -       -       -       Yes
+   D36  PC7     -       -       -       -       -       Yes
+   D37  PC8     -       -       -       -       -       
+
+
+Stub (unfinished).
+
+.. _gpio-recommended-reading:
+
+Recommended Reading
+-------------------
+
+STMicro documentation for STM32F103RB microcontroller:
+
+  * `All <http://www.st.com/mcu/devicedocs-STM32F103RB-110.html>`_
+  * `Datasheet (pdf) <http://www.st.com/stonline/products/literature/ds/13587.pdf>`_
+  * `Reference Manual (pdf) <http://www.st.com/stonline/products/literature/rm/13902.pdf>`_
diff --git a/source/i2c.rst b/source/i2c.rst
index e0444eb..34bd57c 100644
--- a/source/i2c.rst
+++ b/source/i2c.rst
@@ -4,6 +4,4 @@
 |i2c|
 =====
 
-.. |i2c| replace:: I\ :sup:`2`\ C
-
 Stub.
diff --git a/source/language.rst b/source/language.rst
index 8115d6b..6eb5bc7 100644
--- a/source/language.rst
+++ b/source/language.rst
@@ -24,6 +24,9 @@ C or C++ programmers curious about the differences between the Wiring
 language and C++ may wish to skip to the
 :ref:`arduino_c_for_c_hackers`.
 
+.. contents:: Contents
+   :local:
+
 Unique Maple Additions
 ----------------------
 
@@ -308,59 +311,15 @@ Arduino Documentation Links
 .. _const: http://arduino.cc/en/Reference/Const
 .. _sizeof(): http://arduino.cc/en/Reference/Sizeof
 
-.. _pinMode(): http://arduino.cc/en/Reference/PinMode
-.. _digitalWrite(): http://arduino.cc/en/Reference/DigitalWrite
-.. _digitalRead(): http://arduino.cc/en/Reference/DigitalRead
-
-.. _analogReference(): http://arduino.cc/en/Reference/AnalogReference
-.. _analogRead(): http://arduino.cc/en/Reference/AnalogRead
-.. _analogWrite(): http://arduino.cc/en/Reference/AnalogWrite
-
-.. _tone(): http://arduino.cc/en/Reference/Tone
-.. _noTone(): http://arduino.cc/en/Reference/NoTone
-.. _shiftOut(): http://arduino.cc/en/Reference/ShiftOut
-.. _pulseIn(): http://arduino.cc/en/Reference/PulseIn
-
-.. _millis(): http://arduino.cc/en/Reference/Millis
-.. _micros(): http://arduino.cc/en/Reference/Micros
-.. _delay(): http://arduino.cc/en/Reference/Delay
-.. _delayMicroseconds(): http://arduino.cc/en/Reference/DelayMicroseconds
-
-.. _min(): http://arduino.cc/en/Reference/Min
-.. _max(): http://arduino.cc/en/Reference/Max
-.. _abs(): http://arduino.cc/en/Reference/Abs
-.. _constrain(): http://arduino.cc/en/Reference/Constrain
-
-.. _map(): http://arduino.cc/en/Reference/Map
-.. _pow(): http://arduino.cc/en/Reference/Pow
-.. _sqrt(): http://arduino.cc/en/Reference/Sqrt
-
-.. _sin(): http://arduino.cc/en/Reference/Sin
-.. _cos(): http://arduino.cc/en/Reference/Cos
-.. _tan(): http://arduino.cc/en/Reference/Tan
-
-.. _randomSeed(): http://arduino.cc/en/Reference/RandomSeed
-.. _random(): http://arduino.cc/en/Reference/Random
-
-.. _lowByte(): http://arduino.cc/en/Reference/LowByte
-.. _highByte(): http://arduino.cc/en/Reference/HighByte
-.. _bitRead(): http://arduino.cc/en/Reference/BitRead
-.. _bitWrite(): http://arduino.cc/en/Reference/BitWrite
-.. _bitSet(): http://arduino.cc/en/Reference/BitSet
-.. _bitClear(): http://arduino.cc/en/Reference/BitClear
-.. _bit(): http://arduino.cc/en/Reference/Bit
-
+.. Links for the standard Arduino built-in functions are included as
+.. part of the standard epilog.
 .. _our reference page: http://leaflabs.com/docs/external-interrupts/
-.. _attachInterrupt(): http://arduino.cc/en/Reference/AttachInterrupt
-.. _detachInterrupt(): http://arduino.cc/en/Reference/DetachInterrupt
-
-.. _interrupts(): http://arduino.cc/en/Reference/Interrupts
-.. _noInterrupts(): http://arduino.cc/en/Reference/NoInterrupts
 
 .. _Serial: http://arduino.cc/en/Reference/Serial
 .. _community-contributed code: http://www.arduino.cc/playground/Main/GeneralCodeLibrary
 .. _newlib: http://sourceware.org/newlib/
 
+
 .. _arduino_c_for_c_hackers:
 
 Note for C/C++ Programmers
diff --git a/source/libmaple-api.rst b/source/libmaple-api.rst
index af283cb..d5b90b6 100644
--- a/source/libmaple-api.rst
+++ b/source/libmaple-api.rst
@@ -8,3 +8,4 @@ This page documents the lower-level features of libmaple, which may be
 of use to programmers who don't wish to use the Arduino-style
 environment provided by the `Maple IDE <maple-ide-install>`_.
 
+Stub.
diff --git a/source/libmaple.rst b/source/libmaple.rst
index 620fdfa..a018cd7 100644
--- a/source/libmaple.rst
+++ b/source/libmaple.rst
@@ -30,6 +30,8 @@ wrappers and code to imitate the Arduino programming library.
 
     git clone git://github.com/leaflabs/libmaple.git
 
+**Table of contents:**
+
 .. toctree::
    :maxdepth: 2
 
diff --git a/source/libraries.rst b/source/libraries.rst
index c2d5cb0..6a97b0e 100644
--- a/source/libraries.rst
+++ b/source/libraries.rst
@@ -15,8 +15,8 @@ library you want.
 Any incompatibilities between the Maple and Arduino versions are noted
 in the description of the library.
 
-* :ref:`LiquidCrystal <liquid_crystal>`
-* :ref:`Wire <wire>`
+.. contents:: Contents
+   :local:
 
 .. _liquid_crystal:
 
diff --git a/source/maple-ide-install.rst b/source/maple-ide-install.rst
index 46c903b..3c3fffe 100644
--- a/source/maple-ide-install.rst
+++ b/source/maple-ide-install.rst
@@ -11,7 +11,8 @@ check the :ref:`troubleshooting page <troubleshooting>` for help with
 some common problems. If all else fails, try our `forum`_, or `contact
 us directly <http://leaflabs.com/contact>`_!
 
-.. _forum: http://forums.leaflabs.com
+.. contents:: Contents
+   :local:
 
 Download
 --------
diff --git a/source/maple-quickstart.rst b/source/maple-quickstart.rst
index 20d84a0..4d646d7 100644
--- a/source/maple-quickstart.rst
+++ b/source/maple-quickstart.rst
@@ -15,13 +15,8 @@ If you have trouble along the way, try the :ref:`troubleshooting page
 <troubleshooting>` for help with some common problems.  If all else
 fails, try our `forum`_, or `contact us directly <contact>`_!
 
-The steps are:
-
-* :ref:`Install and run the IDE <maple-quickstart-get-ide>`
-
-* :ref:`Compile and upload a program <maple-quickstart-compile-blinky>`
-
-* :ref:`Test the USB serial connection <maple-quickstart-serial-port>`
+.. contents:: Contents
+   :local:
 
 .. _maple-quickstart-get-ide:
 
diff --git a/source/prolog.rst b/source/prolog.rst
new file mode 100644
index 0000000..2823947
--- /dev/null
+++ b/source/prolog.rst
@@ -0,0 +1,7 @@
+.. Additions to this file will be included at the beginning of every
+.. .rst file.  DO NOT USE IT to insert a header; this is not
+.. recommended by the Sphinx people, who have other ways of doing it.
+
+.. Common substitutions
+.. |vcc| replace:: V\ :sub:`cc`
+.. |i2c| replace:: I\ :sup:`2`\ C
diff --git a/source/troubleshooting.rst b/source/troubleshooting.rst
index b878ae4..9d452d1 100644
--- a/source/troubleshooting.rst
+++ b/source/troubleshooting.rst
@@ -2,231 +2,212 @@
 
 .. _troubleshooting:
 
-=======================
- Maple Troubleshooting
-=======================
-
-* :ref:`Hardware Problems <troubleshooting-hardware>`
-
-  * The status LED is throbbing and I can't upload my program!
-  * My board is bricked! I can't upload via the bootloader no matter what!
-  * My 5v peripheral doesn't work! (I2C, SPI, USART, etc)
-  * The reset and D38/serial buttons don't seem to work reliably!
-
-* :ref:`IDE installation problems <troubleshooting-ide-install>`
-
-  * I don't have root/administrator access!
-  * [Linux] I don't use udev!
-
-* :ref:`IDE usage problems <troubleshooting-ide-usage>`
-
-  * [Mac OSX] The "Board" and "Serial Port" menu items are missing!
-
-* :ref:`Common compiler problems <troubleshooting-compilation>`
-
-  * ``NullPointerException``
-  * ``undefined reference to setup()/loop()``
-  * ``error: 'Serial' was not declared in this scope``
-  * ``File(s) not found``
-
-* :ref:`Common upload problems <troubleshooting-upload>`
-
-  * My program is too large!
-  * ``No DFU capable USB device found``
-  * I have multiple Maples installed; how do I know which one will get flashed?
+Troubleshooting
+===============
 
-* :ref:`Command-line issues <troubleshooting-shell>`
+This page documents common problems and their solutions.
 
-  * My flash programs don't seem to stick; they behave like they are RAM!
-  * [Linux] ``cdc_acm 3-1:1.0: no more free acm devices``
+.. contents:: Contents
+   :local:
 
-* :ref:`Tips and tricks <troubleshooting-tips-tricks>`
-
-  * Perpetual bootloader mode
-
-.. _troubleshooting-hardware:
-
-Hardware problems
------------------
+===================
+ Hardware problems
+===================
 
 The status LED is throbbing and I can't upload my program!
+----------------------------------------------------------
 
-    The LED throbs when there has been a failed software
-    :ref:`assertion <language-assert>`.
+The LED throbs when there has been a failed software :ref:`assertion
+<language-assert>`.
 
-    You can still reprogram by resetting the board and uploading
-    during the short window when the bootloader waits for a
-    program.
+You can still reprogram by resetting the board and uploading during
+the short window when the bootloader waits for a program.
 
-    To make this window longer (it can be hard to get the timing
-    right), use :ref:`perpetual bootloader mode
-    <troubleshooting-perpetual-bootloader>`.
+To make this window longer (it can be hard to get the timing right),
+use :ref:`perpetual bootloader mode
+<troubleshooting-perpetual-bootloader>`.
 
 My board is bricked! I can't upload via the bootloader no matter what!
+----------------------------------------------------------------------
 
-    Use the hardcoded serial STM32 serial bootloader to re-flash the
-    bootloader.
+Use the hardcoded serial STM32 serial bootloader to re-flash the
+bootloader.
 
-    .. TODO insert docs on reflashing the bootloader
+.. TODO insert docs on reflashing the bootloader
 
-    If it really is bricked, and you think it's our fault,
-    `contact us <http://leaflabs.com/contact>`_\ !
+If it really is bricked, and you think it's our fault, `contact us
+<http://leaflabs.com/contact>`_\ !
 
 My 5v peripheral doesn't work! (I2C, SPI, USART, etc)
+-----------------------------------------------------
 
-    Yup, the Maple is a 3.3v board. You may need to use a level
-    converter. See the :ref:`compatibility <compatibility>`,
-    :ref:`GPIO <gpio>`, or other :ref:`hardware specific documentation
-    <hardware>` for more information.
+Yup, the Maple is a 3.3v board. You may need to use a level
+converter. See the :ref:`compatibility <compatibility>`, :ref:`GPIO
+<gpio>`, or other :ref:`hardware specific documentation <hardware>`
+for more information.
 
 The reset and D38/serial buttons don't seem to work reliably!
+-------------------------------------------------------------
 
-    A few rev3 boards shipped in May-June 2010 may have had unreliable
-    buttons; see the :ref:`errata page <errata>` for details.  `We're
-    happy to replace these for you <http://leaflabs.com/contact>`_\ !
+A few rev3 boards shipped in May-June 2010 may have had unreliable
+buttons; see the :ref:`errata page <errata>` for details.  `We're
+happy to replace these for you <http://leaflabs.com/contact>`_\ !
 
-.. _troubleshooting-ide-install:
 
-Installation problems
----------------------
+.. _troubleshooting-ide-install:
 
+=======================
+ Installation problems
+=======================
 
 I don't have root/administrator access!
+---------------------------------------
 
-    There are probably hacks or work-arounds to getting programs
-    uploaded without higher level system permissions.  If you can
-    access USB character devices (ACM or ttyUSB style), you should be
-    able to communicate with the Maple and reprogram using an FTDI
-    converter and the serial bootloader, but we haven't tried.
+There are probably hacks or work-arounds to getting programs uploaded
+without higher level system permissions.  If you can access USB
+character devices (ACM or ttyUSB style), you should be able to
+communicate with the Maple and reprogram using an FTDI converter and
+the serial bootloader, but we haven't tried.
 
-    .. TODO: be more helpful
+.. TODO: be more helpful
 
 [Linux] I don't use udev!
+-------------------------
 
-    There is probably a simple way to get autoconfiguration working
-    with devfs; in the meantime, you could try running the entire IDE
-    as root.
+There is probably a simple way to get autoconfiguration working with
+devfs; in the meantime, you could try running the entire IDE as root.
 
-    .. TODO: be more helpful
+.. TODO: be more helpful
 
 .. _troubleshooting-ide-usage:
 
-IDE problems
-------------
+==============
+ IDE problems
+==============
 
-[Mac OSX] The "Board" and "Serial Port" menu items are missing!
+[Mac OS X] The "Board" and "Serial Port" menu items are missing!
+----------------------------------------------------------------
 
-    Sometimes this happens if you try to compile or upload without
-    having a board selected.  The work-around is to restart the
-    IDE. Mysterious!
+Sometimes this happens if you try to compile or upload without having
+a board selected.  The work-around is to restart the IDE. Mysterious!
 
 .. _troubleshooting-compilation:
 
-Common compiler problems
-------------------------
+==========================
+ Common compiler problems
+==========================
 
 ``NullPointerException``
+------------------------
 
-    A classic! Make sure you have selected a board from the pulldown menu. 
+A classic! Make sure you have selected a board from the pulldown menu. 
 
-    .. TODO: remove when Python version is released
+.. TODO: remove when Python version is released
 
 ``undefined reference to setup()/loop()``
+-----------------------------------------
 
-    Your sketch/program either does not include one of the `setup
-    <setup()>`_ or `loop <loop()>`_ functions, or it was not found by
-    the compiler. Your program must include both ``void setup()`` and
-    ``void loop()`` functions; they don't have to do anything, but
-    they **must** be there.
+Your sketch/program either does not include one of the `setup
+<setup()>`_ or `loop <loop()>`_ functions, or it was not found by the
+compiler. Your program must include both ``void setup()`` and ``void
+loop()`` functions; they don't have to do anything, but they **must**
+be there.
 
-    You can start with an example program (to see one in the IDE,
-    click on File > Examples > Stubs > BareMinimum) to get the basic
-    structure.  See also the :ref:`language <language>` documentation.
+You can start with an example program (to see one in the IDE, click on
+File > Examples > Stubs > BareMinimum) to get the basic structure.
+See also the :ref:`language <language>` documentation.
 
-    This is a common error when your entire sketch is blank. 
+This is a common error when your entire sketch is blank.
 
 ``error: 'Serial' was not declared in this scope``
+--------------------------------------------------
 
-    The classic Arduino has only one USART device and uses the unique
-    name "Serial" to control it. Larger devices like the Arduino Mega
-    and the Maple have multiple USARTS referred to as ``Serial1``,
-    ``Serial2``, etc. You probably want ``Serial2`` on the Maple;
-    that's the one connected to pins D0 and D1. See also the
-    :ref:`USART docs <usart>`.
+The classic Arduino has only one USART device and uses the unique name
+"Serial" to control it. Larger devices like the Arduino Mega and the
+Maple have multiple USARTS referred to as ``Serial1``, ``Serial2``,
+etc. You probably want ``Serial2`` on the Maple; that's the one
+connected to pins D0 and D1. See also the :ref:`USART docs <usart>`.
 
 ``File(s) not found``
+---------------------
 
-    There is an intermittent bug with the temporary directory build
-    system that on occasion will lose many of the ``#include``\ d
-    libmaple files. If you recompile everything, it should be fine.
+There is an intermittent bug with the temporary directory build system
+that on occasion will lose many of the ``#include``\ d libmaple
+files. If you recompile everything, it should be fine.
 
-    .. TODO remove when the Python version is released
+.. TODO remove when the Python version is released
 
 .. _troubleshooting-upload:
 
-Common upload problems
-----------------------
+========================
+ Common upload problems
+========================
 
 My program is too large!
+------------------------
 
-    First, make sure you're using the FLASH target instead of RAM;
-    there is several times more FLASH memory available for user
-    programs.
+First, make sure you're using the FLASH target instead of RAM; there
+is several times more FLASH memory available for user programs.
 
 ``No DFU capable USB device found``
+-----------------------------------
 
-    This probably means you don't have a Maple plugged in or powered on! 
+This probably means you don't have a Maple plugged in or powered on! 
 
 I have multiple Maples installed; how do I know which one will get flashed?
+---------------------------------------------------------------------------
 
-    Because the Maple IDE uses DFU to upload programs, you can't
-    select a particular Maple from the Serial Port menu to upload to a
-    particular board. There's no solution to this problem for now:
-    you'll have to just plug in the Maples one at a time. If this is a
-    real problem let us know and we'll see if we can come up with a
-    better solution.
+Because the Maple IDE uses DFU to upload programs, you can't select a
+particular Maple from the Serial Port menu to upload to a particular
+board. There's no solution to this problem for now: you'll have to
+just plug in the Maples one at a time. If this is a real problem let
+us know and we'll see if we can come up with a better solution.
 
 .. _troubleshooting-shell:
 
-Command-line issues
--------------------
+=====================
+ Command-line issues
+=====================
 
 My flash programs don't seem to stick; they behave like they are RAM!
+---------------------------------------------------------------------
 
-    Make sure you :command:`make clean` when switching between FLASH
-    and RAM targets; :command:`make` isn't smart enough to rebuild
-    everything that needs to be for the new target.
+Make sure you :command:`make clean` when switching between FLASH and
+RAM targets; :command:`make` isn't smart enough to rebuild everything
+that needs to be for the new target.
 
 [Linux] ``cdc_acm 3-1:1.0: no more free acm devices``
+-----------------------------------------------------
 
-    This is a nasty one! It means that all 32 possible CDC_ACM serial
-    devices (:file:`/dev/ttyACM25`, etc.) have been used up.
+This is a nasty one! It means that all 32 possible CDC_ACM serial
+devices (:file:`/dev/ttyACM25`, etc.) have been used up.
 
-    The usual cause is using a serial port monitor and not closing it
-    before restarting the Maple or uploading a new program.  The
-    operating system doesn't like that, and locks up that
-    device. After reset the Maple comes back up as a new device. If
-    you develop heavily and don't restart you'll blow right through
-    all 32 devices.
+The usual cause is using a serial port monitor and not closing it
+before restarting the Maple or uploading a new program.  The operating
+system doesn't like that, and locks up that device. After reset the
+Maple comes back up as a new device. If you develop heavily and don't
+restart you'll blow right through all 32 devices.
 
-    The lazy solution is to always close the monitor before
-    restarting, and if you get this error in :file:`dmesg` after a
-    dfu-util "Not Found" error, restart you machine.
+The lazy solution is to always close the monitor before restarting,
+and if you get this error in :file:`dmesg` after a dfu-util "Not
+Found" error, restart you machine.
 
-    The hacker solution is to restart your cdc_acm kernel module. On
-    Ubuntu 09.10, this goes a little something like::
+The hacker solution is to restart your cdc_acm kernel module. On
+Ubuntu 09.10, this goes a little something like::
 
-      $ sudo rmmod cdc-acm
-      $ sudo insmod /lib/modules/2.6.31-20-generic/kernel/drivers/usb/class/cdc-acm.ko
+  $ sudo rmmod cdc-acm
+  $ sudo insmod /lib/modules/2.6.31-20-generic/kernel/drivers/usb/class/cdc-acm.ko
 
 .. _troubleshooting-tips-tricks:
 
-Tips and Tricks
----------------
+=================
+ Tips and Tricks
+=================
 
 .. _troubleshooting-perpetual-bootloader:
 
-**Perpetual Bootloader Mode**
+Perpetual Bootloader Mode
+-------------------------
 
 In this mode, Maple stays a DFU device and does not jump to user code
 until the next reset.  This is useful for guaranteeing that your Maple
@@ -234,13 +215,13 @@ will be available for reprogramming.
 
 To put your Maple into perpetual bootloader mode:
 
-1. Plug your Maple into the USB port.
+#. Plug your Maple into the USB port.
 
-2. Hit the reset button on your Maple (it's the small button at the
-bottom left, labeled RESET).  Notice that it blinks quickly 6 times,
-then blinks slowly a few more times.
+#. Hit the reset button on your Maple (it's the small button at the
+   bottom left, labeled RESET).  Notice that it blinks quickly 6
+   times, then blinks slowly a few more times.
 
-3. Hit reset again, and this time push and hold the other button
-during the 6 fast blinks (the button is on the top right; it is
-labeled BUT). You can release it once the slow blinks start.
+#. Hit reset again, and this time push and hold the other button
+   during the 6 fast blinks (the button is on the top right; it is
+   labeled BUT). You can release it once the slow blinks start.
 
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